17 GPa. J. Geophys. Res. 102, 12252±12263 (1997). 28. Duffy, T. S. & Vaughan, M. T. Elasticity of enstatite and its relationships to crystal structure. J. Geophys. Res. 93, 383±391 (1988). characteristic of cycle seen with E proteorhodopsin Furthermore, Acknowledgements Bacterial Rhodopsin: M. Ferrero and Boudier spectrum of We thank C. Karger for participation in the measurements, and EvidenceF.for a New Type of the and same isosbes for providing the samplesPhototrophy Papua NewSea respectively. The from Baldissero and in the Guinea, Laboratoire de Tectonophysique's EBSD system was funded by the CNRS/INSU, O ded Béjà, et al. dopsin expressed Â Universite of Montpellier Scienceproject , 1902 of an archean craton''. This work II, and NSF 289 ``Anatomy (2000); chemical reactio Â was supported by the CNRS/INSU programme ``Action Thematique Innovante''. D O I: 10.1126/science.289.5486.1902 generate a red-s Correspondence should be addressed to A.T. to that of recomb (e-mail: deia@dstu.univ-montp2.fr). is for your personal, non-commercial use only. This copy ¯ash-photolysis http://www.sciencemag.org/content/289/5486/1902.full existence of pro retinal molecules waters. The photocyc If you wish to distribute this article to others, you can order high-quality copies for and, after hydro colleagues, clients, or custom ers by clicking here . adding all-trans indeed derive fro Permission to republish or repurpose articles or portions of articles can be obta Papers for Today ................................................................. Proteorhodopsin phototrophy following ocean in the the guidelines here . The following resources related to this article are available Â Á Oded Beja*², Elena N. Spudich²³, John L. Spudich³, Marion Leclerc* online at www.scien (this information is current as of May 18, 2010 ): & Edward F. DeLong* 2 orbance (×10–3) Updated information and services, including high-resolution figures, can be found in 1 * version of this article at: Monterey Bay Aquarium Research Institute, Moss Landing, California 95039, 4 USA http://www.sciencem ag.org/cgi/content/full/289/5486/1902 http://www.nature.com/nature/journal/v411/n6839/abs/411786a0.html 0 ³ Department of Microbiology and Molecular Genetics, The University of A list of selected Houston, Texas 77030, the –1 Texas Medical School,additional articles onUSA S cience W eb sites related to this article c Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 ²found authors contributed equally to this work These at:

Papers for Today Bacterial Rhodopsin: Evidence for a New Type of Phototrophy in the Sea O ded Béjà, et al. Science 289, 1902 (2000); D O I: 10.1126/science.289.5486.1902 This copy is for your personal, non-commercial use only. http://www.sciencemag.org/content/289/5486/1902.full If you wish to distribute this article to others, you can order high-quality copies for colleagues, clients, or custom ers by clicking here . Permission to republish or repurpose articles or portions of articles can be obta following the guidelines here . The following resources related to this article are available online at www.scien (this information is current as of May 18, 2010 ): Updated information and services, including high-resolution figures, can be found in version of this article at: http://www.sciencem ag.org/cgi/content/full/289/5486/1902 A list of selected additional articles on the S cience W eb sites related to this article c Slides found at: for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014

Marine Microbe Background • rRNA PCR studies of marine microbes have been extensive • Comparative analysis had revealed many lineages, some very novel, some less so, that were dominant in many, if not all, open ocean samples • Lineages given names based on specific clones: e.g., SAR11, SAR86, etc Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !8

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, June 1991, 0099-2240/91/061707-07$02.00/0 Copyright C) 1991, American Society for Microbiology Vol. 57, No. 6 p. 1707-1713 Phylogenetic Analysis of a Natural Marine Bacterioplankton Population by rRNA Gene Cloning and Sequencing THERESA B. BRITSCHGI AND STEPHEN J. GIOVANNONI* Department of Microbiology, Oregon State University, Corvallis, Oregon 97331 VOL. 57, 1991 Received 5 February 1991/Accepted 25 March 1991 MARINE BACTERIOPLANKTON The identification of the prokaryotic species which constitute marine bacterioplankton communities has been a long-standing problem in marine microbiology. To address this question, we used the polymerase chain CZ reaction to construct and analyze a library of 51 small-subunit (16S) rRNA genes cloned from Sargasso Sea bacterioplankton genomic DNA. Oligonucleotides complementary to conserved regions in the 16S rDNAs of 0._ * C) eubacteria were used to direct the synthesis of polymerase chain reaction products, which were then cloned by u blunt-end ligation into the phagemid vector pBluescript. Restriction fragment length polymorphisms and inmm Vibrio Synechococcus phylogeneticC) groups hybridizations to oligonucleotide probes for the SARll and marine anguillarum 10 0 indicated the presence of at least seven classes of genes. The sequences of five unique rDNAs were determined 0 from completely. In addition to 16S rRNA genes - the marine Synechococcus cluster and the previously identified but uncultivated microbial group, the SARll cluster [S. J. Giovannoni, T. B. Britschgi, C. L. Moyer, and K. G. Field, Nature (London) 345:60-63], two new gene classes were observed. Phylogenetic comparisons indicated that these belonged to unknown species of a- and -y-proteobacteria. The data confirm the earlier crescentus conclusion that a majority of planktonic bacteria are new species previously unrecognized by bacteriologists. 1711 Escherichia coli Vibrio harveyi P. 4.. titative hybridization data which demonstrated that a novel lineage belonging to the oa-proteobacteria was abundant in and amplification of rDNA. A surface (2-m) 0 Collection SAR139 the Sargasso Sea; we also identified novel lineages which bacterioplankton population was collected from hydrostaI I related to cultivated marine Synechococwere very closely S (32° 4'N, 64° 23'W) in the Sargasso Sea as cus spp. (6). In a 0.05 of a study 0coworkers examined clonedhot-spring ecosystem, Ward and tion 0.15 (8). The polymerase chain reaction (24)previously 0.10 was used described fragments of 16S rRNA cDNAs to produce double-stranded rDNA from the mixed-microbiand found numerous novel lineages but no matches to genes al-population Sargasso Sea to representative, cultivated species (2, 6, 18, from the genomic DNA prepared from the plankton FIG. 4. Phylogenetic tree cultivated hot-spring bacteria (33). the rDNA clones from showing relationships of These results sugsample. The amplification and were 30, 31, 32, 35, 40). Positionsthat natural ecosystems in general may include spe- containingregions in the 5' primers regionscomplementary to gested of uncertain homology in regions of the 16S rRNA conserved insertions and 3' deletions were omitted from the analysis. cies which are unknown to microbiologists. Jukes and Cantor The amplification corrects for the effects of superimposed mutations. of Evolutionary distances were calculated by the methoda genetic marker, genes. (15), which primers were the universal 1406R Although any gene may be used as and eubacterial 68F sequence (ACGGGCGGTGTGTRC)rooted with the (TNANAC of Bacillus subtilis (38). distance matrix method ATGCAAGTCGAKCG) The phylogenetic tree was determineddistinctaadvantages. The extensive use of (20). The tree was (17). The reaction conditions were rRNA genes offer by 16S rRNAs for studies of microbial systematics and evoluR. Woese as the as follows: Sequence data not referenced were provided by C.data bases, such and R. Rossen. 1 ,ug of template DNA, 10 ,ul of 10x reaction tion has resulted in large computer buffer (500 mM KCI, 100 mM Tris HCI [pH 9.0 at 250C], 15 RNA Data Base Project, which encompass the phylogenetic mM MgCl2, 0.1% gelatin, 1% Triton X-100), 1 U of Taq DNA diversity found within culture collections. rRNA genes are polymerase (Promega Biological Research Products, Madison, Wis.), 1 ,uM (each) primer, 200 ,uM (each) dATP, dCTP, C, 1 Slides for UC Davis EVE161 CoursedGTP, and dTTP in aJonathan EisenatWinter 2014 Taught by 100-,ul total volume; 1 min 94°chain * min at 72° We Polymerase conserved phyla were Corresponding author. in the corresponding min at 600C, 4 C to C C; 30 cycles. note with caution that some classes 880 phototroph (G - G). D ownloa de d from a e m .a sm .org a t U N IV r SARIOO D ownloa de d from a e m .a sm .org a t U N IV O F C ALIF D AV IS on M a y 1 8 , 2 0 1 0 Oceanospirillum linum SAR 92 Caulobacter SAR83 .0 -bacte- Erythrobacter and therefore can be 0 to examine OCh 114 used Q highly conserved Within the past decade, it has become evident that - Hyphomicrobium vulgare distant phylogenetic relationships with accuracy. The presrioplankton contribute significantly to biomass and bioC) 0 (4, 36). Until ence of large numbers geochemical activity in planktonic systems Rhodopseudomonas marina of ribosomes within cells and the 0 regulation of their biosyntheses in proportion to cellular recently, progress in identifying the microbial species which Rochalimaearates make these molecules ideally O) for ecologsuited growth quintana constitute these communities was slow, because the majore counts) ical studies with nucleic acid ity of the organisms present (as measured by direct Agrobacterium tumefaciens probes. Here we describe the partial analysis of a 16S rDNA cannot be recovered in cultures (5, 14, 16). The discovery a library prepared from photic zone Sargasso Sea bacteriodecade ago that unicellular cyanobacteria are widely distribSARI more recent observation plankton using a uted in the open ocean (34) and the -Es The general approacha for cloning eubacterial Sargasso 16S rDNAs. SAR95 Sea, central oceanic gyre, of abundant marine prochlorophytes (3) have underscored typifies the oligotrophic conditions of the open ocean, prothe uncertainty of our knowledge about bacterioplankton SAR1I microbial community adapted to viding an example of a community structure. low-nutrient conditions. extremely - Liverwort CP The results extend our Molecular approaches are now providing genetic markers previous observations of high genetic diversity among for the dominant bacterial species in natural microbial pop*Anacystis nidulans closely related lineages within this microbial community and ulations (6, 21, 33). The immediate objectives of these rDNA provide - genetic markers for two novel eubacterial studies are twofold: (i) to identify species, both known and Prochlorothrix lineages. novel, by reference to sequence data bases; and (ii) to - SAR6 construct species-specific probes which can be used in 0 quantitative ecological studies (7, 29). * SAR7 p.0 Previously, we reported rRNA genetic markers and quanMATERIALS AND METHODS -

JUlY 1991, p. 4371-4378 0021-9193/91/144371-08$02.00/0 Copyright C) 1991, American Society for Microbiology JOURNAL OF BACTERIOLOGY, Vol. 173, No. 14 Analysis of a Marine Picoplankton Community by 16S rRNA Gene Cloning and Sequencing THOMAS M. SCHMIDT,t EDWARD F. DELONG,t NORMAN R. PACE* Department of Biology and Institute for Molecular and Cellular Biology, Indiana University, Bloomington, Indiana 47405 AND Received 7 January 1991/Accepted 13 May 1991 The phylogenetic diversity of an oligotrophic marine picoplankton community was examined by analyzing the sequences of cloned ribosomal genes. This strategy does not rely on cultivation of the resident microorganisms. Bulk genomic DNA was isolated from picoplankton collected in the north central Pacific Ocean by tangential flow filtration. The mixed-population DNA was fragmented, size fractionated, and cloned into bacteriophage lambda. Thirty-eight clones containing 16S rRNA genes were identified in a screen of 3.2 x 104 recombinant phage, and portions of the rRNA gene were amplified by polymerase chain reaction and D ownloa de d from jb.a sm sequenced. The resulting sequences were used to establish the identities of the picoplankton by comparison with an established data base of rRNA sequences. Fifteen unique eubacterial sequences were obtained, including four from cyanobacteria and eleven from proteobacteria. A single eucaryote related to dinoflagellates was identified; no archaebacterial sequences were detected. The cyanobacterial sequences are all closely related to sequences from cultivated marine Synechococcus strains and with cyanobacterial sequences obtained from the Atlantic Ocean (Sargasso Sea). Several sequences were related to common marine isolates of the y subdivision of proteobacteria. In addition to sequences closely related to those of described bacteria, sequences were obtained from two phylogenetic groups of organisms that are not closely related to any known rRNA sequences from cultivated Slides for UC Davis EVE161 Course Taught by Jonathan Eisen one group within the organisms. Both of these novel phylogenetic clusters are proteobacteria, Winter 2014

DeLong Lab • • Studying Sar86 and other marine plankton Note - published one of first genomic studies of uncultured microbes - in 1996 JOURNAL OF BACTERIOLOGY, Feb. 1996, p. 591–599 0021-9193/96/$04.00 0 Copyright 1996, American Society for Microbiology Vol. 178, No. 3 Characterization of Uncultivated Prokaryotes: Isolation and Analysis of a 40-Kilobase-Pair Genome Fragment from a Planktonic Marine Archaeon JEFFEREY L. STEIN,1* TERENCE L. MARSH,2 KE YING WU,3 HIROAKI SHIZUYA,4 3 AND EDWARD F. DELONG * Recombinant BioCatalysis, Inc., La Jolla, California 920371; Microbiology Department, University of Illinois, Urbana, Illinois 618012; Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California 931063; and Division of Biology, California Institute of Technology, Pasadena, California 911254 Received 14 July 1995/Accepted 14 November 1995 D ownloa de d from One potential approach for characterizing uncultivated prokaryotes from natural assemblages involves genomic analysis of DNA fragments retrieved directly from naturally occurring microbial biomass. In this study, we sought to isolate large genomic fragments from a widely distributed and relatively abundant but as yet uncultivated group of prokaryotes, the planktonic marine Archaea. A fosmid DNA library was prepared from a marine picoplankton assemblage collected at a depth of 200 m in the eastern North Paciﬁc. We identiﬁed a 38.5-kbp recombinant fosmid clone which contained an archaeal small subunit ribosomal DNA gene. Phylogenetic analyses of the small subunit rRNA sequence demonstrated its close relationship to that of previously Slides for UC Davis EVE161 Course coherent group rooted deeply within the Crenarchaeota described planktonic archaea, which form a Taught by Jonathan Eisen Winter 2014

Delong Lab GENOMIC FRAGMENTS FROM PLANKTONIC MARINE ARCHAEA 593 ments isolated from fosmid clones with various restriction endonucle10 kb, the F-factor-based vector the fosmid subfragments. Partial of restriction enzyme to 1 ⇥g of mixture. The reaction mixture was removed at 10, 40, and 60 min. dding 1 ⇥l of 0.5 M EDTA to the e. The partially digested DNA was s described above except using a 1he sizes of the separated fragments n standards. The distances of the d SP6 promoter sites on the excised pmol of T7- or SP6-speciﬁc oligol) and hybridizing with Southern artial sequences reported in Table the following accession numbers: U40243, U40244, and U40245. The and EF2 have been submitted to and U41261. FIG. 1. Flowchart depicting the construction and screening of an environmental library from a mixed picoplankton sample. MW, molecular weight; PFGE, pulsed-ﬁeld gel electrophoresis. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 D ownloa de d from jb.a sm .org a t U N IV O fosmid and pBAC clones digested probed with labeled T7 and SP6 eled subclones and PCR fragments otgun sequencing described above. e estimates from the partial digesof the fosmids and their subclones. and DeSoete distance (9) analyses n using GDE 2.2 and Treetool 1.0, (RDP) (23). DeSoete least squares ng pairwise evolutionary distances, to account for empirical base fretained from the RDP, version 4.0 rRNA sequences were performed the RDP. For distance analyses of lutionary distances were estimated d tree topology was inferred by the n addition and global branch swapprotein sequences, the Phylip proaddition and ordinary parsimony !17

Delong Lab J. BACTERIOL. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 D ownloa de FIG. 4. High-density ﬁlter replica of 2,304 fosmid clones containing approximately 92 million bp of DNA cloned from the mixed picoplankton community. The ﬁlter was probed with the labeled insert from clone 4B7 (dark spot). The lack of other hybridizing clones suggests that contigs of 4B7 are absent from this portion of the library. Similar experiments with the remainder of the library yielded similar results. !18

om the HOT station were mples. Most proteorhodopce waters belonged to the he amino-acid level) to the . In contrast, most of the within the Antarctic clade om the HOT station, HOT E. coli and their absorption m their primary sequences, th the Antarctic clade gave whereas the proteorhodope gave a green (527-nm) al North Paci®c gyre, most with maximal intensity near s maintained over depth, he surface, the energy peak tween 400 and 650 nm. In ows and the half bandwidth m (Fig. 5). Considering the mbers of the two different 0.06 0.05 Absorbance Antarctica (E. F. DeLong, in primers, and sequenced ary sequence analyses based ate that, despite differences on spectra, the Antarctic cterium highly related to bacteria of Monterey Bay10 advantage at different points along the depth-dependent light 0.04 HOT 75 m Antarctica 0.03 HOT 0 m 0.02 Monterey Bay 0.01 1.0 Relative irradiance opsins. Furthermore, palE6 to its Monterey Bay d transport of protons in udich et al., manuscript in 5m 0.8 0.6 75 m 0.4 0.2 0 350 400 450 500 550 600 650 Wavelength (nm) Figure 5 Absorption spectra of retinal-reconstituted proteorhodopsins in E. coli membranes. All-trans retinal (2.5 mM) was added to membrane suspensions in 100 mM phosphate buffer, pH 7.0, and absorption spectra were recorded. Top, four spectra for palE6 (Antarctica), HOT 75m4, HOT 0m1, and BAC 31A8 (Monterey Bay) at 1 h after retinal addition. Bottom, downwelling irradiance from HOT station measured at six wavelengths (412, 443, 490, 510, 555 and 665 nm) and at two depths, for the same depths and date that the HOT samples were collected (0 and 75 m). Irradiance is plotted relative to irradiance at 490 nm. Slides for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014

articles Community structure and metabolism through reconstruction of microbial genomes from the environment Gene W. Tyson1, Jarrod Chapman3,4, Philip Hugenholtz1, Eric E. Allen1, Rachna J. Ram1, Paul M. Richardson4, Victor V. Solovyev4, Edward M. Rubin4, Daniel S. Rokhsar3,4 & Jillian F. Banﬁeld1,2 1 Department of Environmental Science, Policy and Management, 2Department of Earth and Planetary Sciences, and 3Department of Physics, University of California, Berkeley, California 94720, USA 4 Joint Genome Institute, Walnut Creek, California 94598, USA ........................................................................................................................................................................................................................... RESEARCH ARTICLE Microbial communities are vital in the functioning of all ecosystems; however, most microorganisms are uncultivated, and their roles in natural systems are unclear. Here, using random shotgun sequencing of DNA from a natural acidophilic bioﬁlm, we report reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II, and partial recovery of three other genomes. This was possible because the bioﬁlm was dominated by a small number of species populations and the frequency of genomic rearrangements and gene insertions or deletions was relatively low. Because each sequence read came from a different individual, we could determine that single-nucleotide polymorphisms are the predominant form of heterogeneity at the strain level. The Leptospirillum group II genome had remarkably few nucleotide polymorphisms, despite the existence of low-abundance variants. The Ferroplasma type II genome seems to be a composite from three ancestral strains that have undergone homologous recombination to form a large population of mosaic genomes. Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen ﬁxation and energy generation, and provided insights into survival strategies in an extreme environment. 1 1 3 Environmental Genome Shotgun Sequencing of the Sargasso Sea J. Craig Venter, * Karin Remington, John F. Heidelberg, Aaron L. Halpern,2 Doug Rusch,2 Jonathan A. Eisen,3 The study of microbial evolution and ecology has been revolutio- ﬂuorescence in situ hybridization (FISH) revealed that all bioﬁlms Dongying Wu,3 Ian Paulsen,3 Karen E. Nelson,3 William Nelson,3 nized by DNA sequencing and analysis1–3. However, isolates have contained mixtures of bacteria (Leptospirillum, Sulfobacillus and, in Derrick few cases, 3 Samuel Levy,2 archaea (Ferroplasma 6 been the main source of sequence data, and only a small fraction of aE. Fouts, Acidimicrobium) andAnthony H. Knap,and other 4–6 has members of the Thermoplasmatales). The genome of one microorganisms have been cultivated . Consequently, focusMichael W. Lomas,6 Ken Nealson,5 Owen White,3 of these shifted towards the analysis of uncultivated microorganisms via archaea, Ferroplasma acidarmanus 1 Rachel Parsons,6 Jeremy Peterson,3 Jeff Hoffman, fer1, isolated from the Richmond cloning of conserved genes5 and genome fragments directly from mine, has been sequenced previously (http://www.jgi.doe.gov/JGI_ 4 Holly Baden-Tillson,1 Cynthia Pfannkoch,1 Yu-Hui the environment7–9. To date, only a small fraction of genes have been microbial/html/ferroplasma/ferro_homepage.html).Rogers, Slides for UC Davis EVE161 Course bioﬁlm (Fig.Jonathan 1 of AMD communities was Hamilton 1a) typical recovered from individual environments, limiting the analysis of A pink Taught by O. Smith Eisen Winter 2014 chlorococcus, tha photosynthetic bio Surface water were collected ab from three sites o February 2003. A lected aboard the S station S” in May are indicated on F S1; sampling prot one expedition to was extracted from genomic libraries w 2 to 6 kb were m !37 prepared plasmid

two groups of scaffolds representing two disSargasso Sea related to the published tinct strains closely at depths ranging from 4ϫ to 36ϫ (indicated with shading in table S3 with nine depicted in Fig. 1. MODIS-Aqua satellite image of ocean chlorophyll in the Sargasso Sea grid about the BATS site from 22 February 2003. The station locations are overlain with their respective identiﬁcations. Note the elevated levels of chlorophyll (green color shades) around station 3, which are not present around stations 11 and 13. http://www.sciencemag.org/content/304/5667/66 Fig. 2. Gene conserSlides vation among closely for UC Davis EVE161 Course Taught by Jonathan Eisen Winter 2014 !42

sequence when they would otherwise be labeled as repetitive. We evaluated our final assembly Table 1. Gene count results in a tiered fashion, looking at well-sampled breakdown by TIGR role genomic those found on ascategory. Gene set includes regions separately from those barely sampled at our current level of sequencing. semblies from samples 1 to 41.66 million sequencesreads the The and fragment from from samples 5 to 7. AWeatherbird II samples (table S1; samples 1 to more detailed table, sep4; stations 3, 11, and 13), were pooled and arating Weatherbird II samplesto providethe Sorcerer II assembled from a single master assembly samples is presented in for comparative purposes. The assembly generthe SOM (table S4). Note ated 64,398 scaffolds ranging size from 826 that there are 28,023 genes which were 256inMbp of unique bp to 2.1 Mbp, containing classiﬁed sequence and in more than one role category.spanning 400 Mbp. After assembly, there remained 217,015 paired-end reads, or “mini-scaffolds,” spanning 820.7 Mbp as well as an additional 215,038 unassembled sinTotal gleton TIGR role category reads covering 169.9 Mbp (table S2, genes column 1). The Sorcerer II samples provided almost no assembly, so we consider for these samples only the 153,458 mini-scaffolds, spanAmino acid biosynthesis 518.4 Mbp, and the remaining 18,692 37,118 ning singleton reads (table S2, column 2). In total, Biosynthesis of cofactors, 25,905 1.045 Gbp of nonredundant sequence was genprosthetic groups, and carriers of overlapping reads within the erated. The lack unassembled set indicates that lack of additionCell envelope 27,883 al assembly was not due to algorithmic limitaCellular processes 17,260 tions but to the relatively limited depth of sequencing coverage Central intermediary metabolism given the level of diversity 13,639 within the sample. DNA metabolism 25,346 The whole-genome shotgun (WGS) assembly has been deposited at DDBJ/EMBL/GenBank Energy metabolism 69,718 under Fatty acid and phospholipidthe project accession AACY00000000, 18,558 and all traces have been deposited in a corresponding TraceDB trace archive. The version metabolism described paper is the first version, Mobile and extrachromosomalin this Unlike a conventional WGS 1,061 AACY01000000. element functions entry, we have deposited not just contigs and scaffolds but the unassembled paired singletons Protein fate 28,768 and individual singletons in order to accurateProtein synthesis 48,012 ly reflect the diversity in the sample and allow searches Purines, pyrimidines, nucleosides,across the entire sample with19,912 in a single database. and nucleotides Genomes and large assemblies. Our analysis first focused on the well-sampled geRegulatory functions nomes

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